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dputhier / pygtftk

A python package and a set of shell commands to handle GTF files
GNU General Public License v3.0
45 stars 6 forks source link

Add a diagram that display both S and N #86

Closed dputhier closed 5 years ago

dputhier commented 5 years ago

Any idea ? Maybe a simple scatter plot...

qferre commented 5 years ago

I think simple ideas can be the best. A simple scatter plot of the fold change of N vs the fold change of S might be enough. We could plot log(FC) or 1/FC or any other transformation to emphasize small differences.

dputhier commented 5 years ago

I added a volcano as suggested by Guillaume.

As it requires to compute -log10(pval) I have changed the pval == 0 to 1e-320 (just for plotting the diagram). @qferre tell me if its ok to set them to1e-320 . The N and S statistics are treated in the same plot:

image

Note that the current implementation of ggrepel in plotnine seems to be still in dev so I'm using transparent labels at the moment...

41137fbd349fcf778a1d8cc02a409a9d1c50fadd

qferre commented 5 years ago

Putting them at 1e-320 should be okay. I did the same modification for the histograms. Great job :) Could you add it to the documentation as an example ?

dputhier commented 5 years ago

It will be included in the html frame in which the pdf output is enclosed. I was thinking about adding it to the homepage of the doc (?).

qferre commented 5 years ago

Sounds like a good idea to me :)